Alabasta and Enies Lobby/Water 7 would have to be the ones I prefer most. The whole rebel army thing I enjoyed and Crocodile is hands down an awesome villain. As for Enies Lobby/Water 7, I mostly enjoyed the actual Enies section with the big battles going on there, good stuff.
As for skypiea and Thriller Bark, while I enjoyed them towards the end I found the beginning and middle parts of them extremely boring.
tl;dr: I seem to prefer the arcs where more than just the Strawhats and one other group are against each other; the current arc seems to be as such.